BioSimSpace.Metadynamics.CollectiveVariable.Torsion

class BioSimSpace.Metadynamics.CollectiveVariable.Torsion(atoms, hill_width=0.3500 radians, lower_bound=None, upper_bound=None, grid=None, pbc=True)

A class for torsion based collective variables.

__init__(atoms, hill_width=0.3500 radians, lower_bound=None, upper_bound=None, grid=None, pbc=True)

Constructor.

Parameters
  • atoms ([int, int, int, int]) – The indices of the four atoms involved in the torsion.

  • hill_width (Angle) – The width of the Gaussian hill used to sample this variable.

  • lower_bound (Bound) – A lower bound on the value of the collective variable.

  • upper_bound (Bound) – An upper bound on the value of the collective variable.

  • grid (Grid) – The grid on which the collective variable will be sampled. This can help speed up long metadynamics simulations where the number of Gaussian kernels can become prohibitive.

  • pbc (bool) – Whether to use periodic boundary conditions when computing the collective variable.

Methods

__init__(atoms[, hill_width, lower_bound, …])

Constructor.

getAtoms()

Return list of atom indices involved in the torsion.

getGrid()

Get the grid on which the collective variable is sampled.

getHillWidth()

Return the width of the Gaussian hill used to bias this collective variable.

getLowerBound()

Get the lower bound on the collective variable.

getPeriodicBoundaries()

Return whether to take account of periodic boundary conditions when computing the collective variable.

getUpperBound()

Get the upper bound on the collective variable.

nComponents()

Return the number of components for the collective variable.

setAtoms(atoms)

Set the atoms for which the torsion will be calculated.

setGrid([grid])

Set a grid on which the collective variable will be sampled.

setHillWidth(hill_width)

Set the width of the Gaussian hills used to bias this collective variable.

setLowerBound([lower_bound])

Set a lower bound on the value of the collective variable.

setPeriodicBoundaries(pbc)

Set whether to use periodic_boundaries when calculating the collective variable.

setUpperBound([upper_bound])

Set an upper bound on the value of the collective variable.

getAtoms()

Return list of atom indices involved in the torsion.

Returns

atoms – The atom indices involved in the torsion.

Return type

[int, int, int, int]

getGrid()

Get the grid on which the collective variable is sampled.

Returns

grid – The grid on which the collective variable is sampled.

Return type

Grid

getHillWidth()

Return the width of the Gaussian hill used to bias this collective variable.

Returns

hill_width – The width of the Gaussian hill.

Return type

Angle

getLowerBound()

Get the lower bound on the collective variable.

Returns

lower_bound – The lower bound on the value of the collective variable.

Return type

Bound

getPeriodicBoundaries()

Return whether to take account of periodic boundary conditions when computing the collective variable.

Returns

pbc – Whether to use periodic boundaries conditions.

Return type

bool

getUpperBound()

Get the upper bound on the collective variable.

Returns

upper_bound – The upper bound on the value of the collective variable.

Return type

Bound

nComponents()

Return the number of components for the collective variable.

setAtoms(atoms)

Set the atoms for which the torsion will be calculated. measured.

Parameters

atoms ([int, int, int, int]) – The atoms involved in the torsion. will be measured from.

setGrid(grid=None)

Set a grid on which the collective variable will be sampled. Call with no arguments to clear the grid.

Parameters

grid (Grid) – A grid for the collective variable.

setHillWidth(hill_width)

Set the width of the Gaussian hills used to bias this collective variable.

hill_widthAngle

The width of the Gaussian hill.

setLowerBound(lower_bound=None)

Set a lower bound on the value of the collective variable.

Parameters

lower_bound (Bound) – A lower bound on the value of the collective variable.

setPeriodicBoundaries(pbc)

Set whether to use periodic_boundaries when calculating the collective variable.

Parameters

pbc (bool) – Whether to use periodic boundaries conditions.

setUpperBound(upper_bound=None)

Set an upper bound on the value of the collective variable.

Parameters

upper_bound (Bound) – An upper bound on the value of the collective variable.